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Me, Microbes, and I

It has been said that “No man is an island.” While you may quibble that it should be “No one is an island,” we know what it means: We human beings depend on one another. We depend on each other, and we also depend on ecosystems to provide us with water and clean air—among other things. Yet there are other important ecosystems within us and on us.

You are no island: no, you are more of a continent complete with colonists, invaders, battles for resources, and turf wars. And there are a lot more of “them” than there are of “you,” about one hundred trillion of them. As one article in the Economist put the idea, “…humans are not single organisms, but superorganisms made up of lots of smaller organisms working together.”

Microbes (Photo credit: Wikipedia)

We have known for a long time that our guts harbor “good” bacteria (yogurt companies advertise about probiotics) and health officials caution against unnecessarily taking antibiotics which could harm good bacteria. These bacteria, it turns out, have evolved along with us (Homo sapiens) and are part of our being. And, in turn, our bacteria evolve within us, having numerous generations during a person’s lifespan, and adapting to changing conditions.

What is now coming out of research is how essential those bacteria are to our physical and mental health. For instance, on our skin, “Staphylococcus epidermidis fends off skin infection and enhances immunity,” the Economist article says. Maybe that antibacterial soap isn’t your best choice for healthy skin.

Researchers call the symbiotic relationship that microbes have with particular animals or plants a microbiome. The sheer magnitude and diversity of your microbiome is staggering. “The typical human is home to a vast array of microbes,” evolutionary biologist Olivia Judson wrote in the New York Times. “If you were to count them, you’d find that microbial cells outnumber your own by a factor of 10. On a cell-by-cell basis, then, you are only 10 percent human. For the rest, you are microbial.” A human being has 23,000 different genes. Our microbiome has almost 150 times that number, about three million genes.

In their proper places, microbiomes are truly symbiotic, a collaboration of human and micro-critter. We provide hospitable living conditions, and the microbes help break down foods for digestion, synthesize vitamins, and help our immune system. Inoculation with microbiota begins when we travel through the birth canal. Among other things, our new gut bacteria will “affect the wiring of nerves in the stress system, influencing how the body reacts to stress for the rest of its life,” writes Tom Siegfried in Science News. Our mothers’ influence, then, goes even further than we knew.

When they are not in their proper place or when unwanted bacteria come in, the results can be distressing, painful, or even deadly for the host. Researchers have linked off-kilter microbiomes to obesity, diabetes, heart disease, autism, and some autoimmune diseases.

Rejiggering some microbiomes apparently cures some diseases. “The past few years have shown that having good relations with the 100 trillion bacteria which inhabit the gut is essential to human health,” reports an Economist article. “If relations break down, hostile bacteria may invade and previously friendly ones may turn hostile. When things do go wrong, though, doses of corrective bacteria can make a difference.”

The method of delivery for healthy bacteria to the intestine is rather yucky. Yes, eating yogurt with probiotics can help people with irritable bowel syndrome, but pretty much everything else requires a fecal transplant—a “trans-poo-sion,” if you will. Gastroenterologist Thomas Borody says, “By implanting another person’s stool, that other person may contain bacteria which manufacture antibiotics. And this is the key: bacteria make molecules that kill other bacteria. In fact, most antibiotics come from bacteria.” Fecal transplants can change the gut’s microbiome, and this changes our health.

Scientists have just begun to understand our microbiome’s interaction with us. For one thing, there is much to learn simply due to the number of these critters. “The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies,” one scientific abstract says. We are also at the beginning of this scientific process; a time that is analogous to when people knew willow tree bark relieved headaches but had not yet identified acetylsalicylic acid (the active ingredient in aspirin) as the reason.

Our microbiomes and earth’s biomes (plants and animals found in particular habitats) have evolved and continue to evolve as conditions change. Understanding their complexities will help improve our lives. And, as always, more research is needed.

You know, medicine is not an exact science, but we are learning all the time. Why, just fifty years ago, they thought a disease like your daughter’s was caused by demonic possession or witchcraft. But nowadays we know that Isabelle is suffering from an imbalance of bodily humors, perhaps caused by a toad or a small dwarf living in her stomach.

Perelman School of Medicine at the University of Pennsylvania. (2012, March 15). Genetic Variation in Human Gut Viruses Could be Raw Material for Inner Evolution, Perelman School of Medicine Study Finds. Retrieved June 13, 2013, from Penn Medicine: http://www.uphs.upenn.edu/news/News_Releases/2012/03/bushman/

PsMag. Our Destiny Lies Not in Our Stars, But in Our Bacteria. http://www.psmag.com/environment/our-destiny-lies-not-in-our-stars-but-in-our-bacteria-62968

Siegfried, T. (2013, May 28). Microbes at home in your gut may also be influencing your brain. Retrieved June 4, 2013, from Science News: http://www.sciencenews.org/view/generic/id/350674/description/Microbes_at_home_in_your_gut_may_also_be_influencing_your_brain

The Economist. (2013, February 21). Evolution: History Repeating. Retrieved June 7, 2013, from The Economist: http://www.economist.com/blogs/babbage/2013/02/evolution

The Economist. (2013, April 11). Microbes and men: Consumer microbiomics . Retrieved June 6, 2013, from The Economist: http://www.economist.com/blogs/babbage/2013/04/microbes-and-men

The Economist. (2012, August 18). The human microbiome: Me, myself, us. Retrieved June 4, 2013, from The Economist: http://www.economist.com/node/21560523

The Economist. (2012, November 3). Treating disease with microbes: Bugs in the system. Retrieved June 4, 2013, from The Economist: http://www.economist.com/news/science-and-technology/21565586-bacterial-medicine-starting-emerge-bugs-system

Virginia Tech. (2013, February 8). Villain stomach bug may have a sweet side. Retrieved June 6, 2013, from EurekaAlert!: http://www.eurekalert.org/pub_releases/2013-02/vt-vsb020813.php

Zimmer, C. (2006, January 3). From Bacteria to Us: What Went Right When Humans Started to Evolve? Retrieved June 4, 2013, from New York Times: http://www.nytimes.com/2006/01/03/science/03zimm.html?_r=0

The guts of humans and other mammals contain thriving trillions of bacteria and other microbes. One of these Very Important Prokaryotes is called Akkermansia muciniphila. Akkermansia accounts for 3 to 5 percent of the bacteria in a normal gut, making it one of our more common intestinal microbes. And it seems to wield a strong influence on our body weight.

What the preferred ecological niche or host (if any) of clades II–V is and whether the clades actually can persist in the external environment in the absence of fecal inputs (i.e., represent truly free-living bacteria) remain elusive, and additional data need to be collected before more robust conclusions can emerge. For instance, strains of clades II–V have been recovered occasionally from birds and ruminant mammals ( 9 ), but the extent to which these results are influenced by the processes of strain migration and extinction (as opposed to persistence within the host) is unclear. What our genomic data as well as data from physiological studies and environmental surveys performed previously ( 9 , 13 ) suggest is that clades II–V are better at surviving in the external environment than is commensal E. coli and are poor competitors in the human gastrointestinal tract relative to successful clonal complexes such as those represented by CFT073 and MG1555 strains. Therefore, clades II–V are highly unlikely to represent a risk to public health.

The best phrase I saw for fecal transplants was from an experiment where they created a mix of microbes thought to mimic the make up of a human sample, but without the further risk of something bad coming along. It was called “sham poo” among the twitterati. Still cracks me up. But has not seemed to catch on….

Good post. Amazing that medical science knows so little about this subject. We have some general knowledge that was outlined in your article but when it comes to really understanding how to properly take care of our gut bugs there is little real science.

An analogy might be what it takes to grow good food. You need good soil, sun, water, temps, etc. There are indicators we associate with healthy soil for example, we think the presence of worms means there is the right amount of moisture, organic matter, etc.

For our gut bacteria, what do we really need to properly care for it in terms of diet, water, exercise, fasting, etc? Is there any real science on this?

Transplanting someone else’s into us seems like one of those crazy approaches akin to fixing the symptom but not the disease. Maybe it is a solution in extreme cases, but, what should we be doing on a daily basis?

I read The Economist article and then started reading and researching more about our microbiome, so I decided to put it in my Record-Bee column. I expect it will be in tomorrow’s edition (or next Tuesday’s). The idea that we contained biomes just as our world does fascinated me, so I wrote about it, thinking it might fascinate some readers too. I don’t know if I will write more about it. I try to stick to an environmental beat, this seemed to have enough crossover that it sort of fit. If the microbiome has more applicability to how we view our biomes, I might write something.

You bring up a good question: Fecal transplants may be “a solution in extreme cases, but, what should we be doing on a daily basis?” That’s a really good question. Quacks, well-meaning folks, and charlatans are making money telling us they know how to eat just right. Personally, I’m doubtful and quite skeptical of a one-size-fits-all diet. What I’m doing is watching for signs and symptoms and then getting as much information as I can as to how to proceed.

If our microbiomes are analogous to nature there may be no one correct way to eat. We know that nature is never in balance. That biomes and their ecosystems are constantly adapting. “[S]cience has now resolved the great early 20th century debate between “balance of nature” ecologist Frederic Clements and ecosystem dynamist Henry Gleason in favor of Gleason,” Ronald Bailey wrote. Gleasons thesis is “ecosystems were assembled by chance depending on what species got there first and were successful in competing with other species as they arrived.” Our cultural and genetic makeup also affects how our microbiomes respond to inputs.

You mention healthy soil and the presence of worms. Here in California that’s certainly the case, but I read that the forests in (if memory serves) the Upper Peninsula of Minnesota’s forests were being invaded by earthworms dumped or lost by fishermen (and women, but mostly men). Those forests don’t naturally have earthworms and their presence was creating problems. But, you’re right, earthworms are great for our gardens.

I think the knowledge just opens up more for us to be aware of and may be a breakthrough in treating some of the more chronic diseases. As the Economist notes in Treating disease with microbes: Bugs in the system:
“If they [bacterial mixing treatments] do work, they may open avenues for the bacterial treatment of other conditions linked to gut bacteria. These conditions include obesity, diabetes and even, possibly, autism. A new era of bacterial medicine could thus be about to dawn.”

I agree with your assessments on personal diet, ecosystems, and the plethora of misinformation on the subject. On one level probiotics make sense but are the ones being sold really right for me? It seems that on a personal level we would want to know at what PH the beneficial microbes thrive, monitor the PH of our system, adjust our diet to maintain the right PH, and then try to figure out which foods tend to have the microbes we need and/or provide the sustenance those microbes want.

That is just what I can think of off the top of my head while writing this. Understanding the above by having a tool set easily accessible (inexpensive) and knowing in general what microbes my body should have does not really seem like a tall order in this day and age.